RNA Designer takes as input a secondary structure description and outputs an RNA strand that is predicted to fold to that secondary structure. RNA Designer can be used to design RNA molecules with certain structural properties, as part of the development of molecules with novel functional properties, or more fundamentally in order to understand which secondary structure elements are critical to specific functions of cellular RNAs. RNA Designer uses a stochastic local search algorithm, which decomposes the input structure in a hierarchical fashion, finds strands that fold to the resulting substructures, and then attempts to combine the strands for substructures into a strand for the overall structure. RNA Designer uses the Fold software from the Vienna Package [2] as part of its implementation.


Reference.

Mirela Andronescu, Anthony P. Fejes, Frank Hutter, Holger H. Hoos and Anne Condon, ``A new algorithm for RNA secondary structure design'', Journal of Molecular Biology, 336 (3): 607-624, Feb 2004


Other references and links

[1] Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, L. Sebastian Bonhoeffer, Manfred Tacker, and Peter Schuster, Fast Folding and Comparison of RNA Secondary Structures, Monatsh.Chem. 125: 167-188 (1994).

Vienna RNA Package